The following version of this book was used to create this study guide: Groff, Lauren. Matrix. New York: Riverhead Books, 2021.

When the novel begins it is 1158, and the protagonist, Marie, is 17 years old and has just arrived at the abbey where she is to live. Marie is originally from Le Main, France, where she was raised by her mother and aunts who fought in the Second Crusade. Marie's mother died when she was 12 and Marie managed her estate for two years before the death was discovered. Afterward, she was sent to the English court at Westminster, where she was living with her half-brother, who is the king of England, and his wife, Queen Eleanor (a character based on the real-life Eleanor of Aquitaine). Marie is distraught because she is in love with Eleanor and because Eleanor sent her away to live in the abbey despite the fact that she has “no godly avocation whatsoever” (5). She has also left behind her servant Cecily, with whom she was in a romantic relationship.

The abbey is impoverished, and the nuns living there are dying of starvation and disease. Marie is greeted by Abbess Emme and Subprioress Goda. She is distraught, but she makes friends with another novice nun named Ruth. Marie decides to write a collection of poems to send to Eleanor, believing this will result in her being invited back to court. However, this does not occur. Instead, Marie hears the nuns singing in the chapel one day and considers the possibility of committing herself to life at the abbey. She looks at the accounting books and realizes none of the tenants living on the surrounding land are paying rent. She goes to one delinquent family's house and forcibly removes them from the property. Afterward, the other tenants pay what they owe.

The nuns learn that one of their fields is blighted and Marie accompanies Abbess Emme to perform a ritual intended to assuage the anxieties of the people living in the surrounding town, who might think the blight is evidence of witchcraft or the devil. Afterward, Marie decides to fully commit herself to the abbey, using Eleanor as a “model” (60) for becoming a powerful woman herself. Marie takes the veil and life at the abbey improves under her management. She meets a child named Wulfhild and invites her live at the abbey as an oblate.

When Marie is 35, Wulfhild turns 18 and leaves the abbey to marry. Marie makes her the abbey's bailiffess, in charge of handling Marie's business in town and collecting the rents. Shortly thereafter, Marie breaks her tooth on an apricot pit and goes to the infirmary. The infirmatrix, Nest, removes the tooth and then the two have a sexual encounter. A new nun arrives at the abbey named Tilde. She is a cousin of Eleanor's. The abbey has become wealthy. Abbess Emme dies and Marie is elected abbess to replace her.

Marie is 47 and she has a religious vision featuring the Virgin Mary and a rose that she believes suggests she should build a labyrinth around the abbey so it is impenetrable to outsiders. Ruth and Wulfhild are skeptical, but everyone ultimately agrees to the plan and the labyrinth is constructed. Marie has a second vision featuring the Virgin Mary and Eve that foretells a visit from Eleanor.

Eleanor arrives and she and Marie discuss the challenges of being a powerful woman in a patriarchal society. When Eleanor leaves, Marie feels that she is no longer angry with her as she was for years after being sent to the abbey. Eleanor's husband has died and her son is now king. When Eleanor leaves, Marie travels through the newly completed labyrinth and feels proud of her achievement.

Shortly thereafter, a group of men from town attempt to breach the labyrinth. Marie, having been warned ahead of time by her spies, sends the nuns and female tenants to protect the labyrinth. They fight the men off, but a tenant is killed in the process.

Marie has another vision, which she interprets as a suggestion that she build a new wing of the abbey, called the abbess house. Stonemasons are hired to assist with the construction. A new novice arrives, named Avice, whose parents caught her having sex with a man. Marie is profoundly attracted to the girl, who resembles Eleanor. Later, it is revealed that Avice is pregnant, presumably after having sex with a stonemason. She dies in childbirth and the baby is stillborn.

There is a fire in town that kills the entire church staff that was serving the abbey so there is no one to preside over mass and confession. Marie decides to perform these rites herself, and many of the nuns find this infuriating, but they are loyal and do not report Marie to the Church authorities.

Marie is aging and she learns that Eleanor is near death. Another novice, Sprota, arrives, and she is believed to be especially holy. She is popular with the other novices and nuns but Marie thinks her piety is an act. Fearing Sprota could challenge her authority, Marie announces her plan to establish a leper house in town and for Sprota to attend to the lepers. As Marie predicted, Sprota flees from the leper house, never to be seen again at the abbey.

Eleanor dies. Marie, inconsolable in her grief, conceives of another project—a dam to run water to the abbey. This project is put into action, but Wulfhild overexerts herself and becomes ill. She dies soon after and Marie blames herself.

When Marie is 71, Tilde invites Marie's old servant Cecily to stay in the abbey. Marie spends her final days with the woman she loved long ago. Marie develops cancer and dies.

After her death, Tilde is elevated to abbess. She finds Marie's journal, where she had written about her visions. She burns the journal. The inhabitants of the abbey contemplate Marie's legacy and believe her to be akin to a saint.